That "extension" is the main part of Vivaldi which checks for Flash content.
There is no problem of Flash blocking at all if you enable Flash in vivaldi://chrome/settings/content or in section Plugins of vivaldi://settings/webpages/.

But, judging from where it's placed & it's there since beginning. Probably source code level.
If the code was Vivaldi part, then the only way we could do is "feature request" it. Closed source for this part. Except you're invited to be dev.